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X-ray structure of human prostate-specific membrane antigen(PSMA) in complex with a inhibitor Glu-490
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BI1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 34% (v/v) pentaerythritol propoxylate PO/OH 5/4
1 % (w/v) PEG 3350
100 mM Tris-HCl, pH 8.0
Crystal Properties Matthews coefficient Solvent content 3.3 62.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.54 α = 90 b = 130.103 β = 90 c = 158.91 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 2M 2020-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.9184 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.73 50 99.6 0.999 14.43 4.5 109170
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.73 1.83 98.9 0.869 1.99 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 3BI1 1.73 46.96 106994 2101 99.52 0.1636 0.1632 0.1711 0.1833 0.1874 RANDOM 36.467
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 1.08 -2.29 1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.757 r_dihedral_angle_4_deg 14.515 r_dihedral_angle_3_deg 14.014 r_dihedral_angle_1_deg 6.108 r_angle_refined_deg 1.712 r_chiral_restr 0.125 r_bond_refined_d 0.017 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5529 Nucleic Acid Atoms Solvent Atoms 468 Heterogen Atoms 318
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing